This article covers everything you need to know about the gut microbiome, including what it is, why it is SO important for your health, and how to maintain a healthy gut.

Believe it or not, your body contains more bacteria cells in it than human cells. (…about 10x more!)

Don’t worry, you’re still human, you’re just home to trillions of tiny bacterial cells happily living inside.

Most of these bacteria hang out in your gut, and make up what is known as the gut microbiome.

However, research continues to show that these gut bacteria are not just hanging out; they do a lot more for our bodies than we could ever imagine.

It turns out these bacteria are working away alongside you all the time, influencing your normal body functioning, your susceptibility to disease, and almost every other aspect of your health.

The state of your gut microbiome is one of the most critical determining factors of the state of your health. Some experts even go so far as to suggest all health problems stem from the gut.

What is The Gut Microbiome?

The gut microbiome is the collection of all the microorganisms (such as bacteria, fungi, and viruses) that live in your gastrointestinal tract.

Side note: Technically, the gut microbiota is the collection of all the microorganisms in the gut, whereas the gut microbiome is the collection of all the microorganisms and their genetic material in the gut. But these two terms are commonly used interchangeably, so we won’t focus on the difference between them in this article.

Bacteria are the most well studied of the microorganisms in the gut, so we’ll be focusing on them.

Why is The Gut Microbiome Important?

When you think of bacteria, you may think of disease. While some bacteria species certainly do cause diseases and health problems, many others are absolutely crucial for your health.

Both “good” and “bad” bacteria live in the gut, but as long as the bacteria populations in the gut remain balanced (i.e. enough good bacteria, not too many bad bacteria), they will work in harmony with our bodies, for the most part.

It is when the microbiome is disrupted or unbalanced (known as gut dysbiosis) that problems can occur.

Let’s look at some of the many ways the gut microbiome affects human health.

7 Ways Your Gut Microbiome Can Affect Your Health

1. Digestion

Gut bacteria are beneficial to many aspects of our digestion and nutrition, including nutrient absorption, nutrient synthesis, enzyme synthesis, digestion of substances that are indigestible to us, and production of other molecules (like amino acids) that are important for keeping us healthy.

Some gut bacteria are able to ferment dietary fibres (which are non-digestible to us) and produce short-chain fatty acids. Short-chain fatty acids are very important for maintaining healthy intestines and a balanced gut. So important, in fact, that their absence is linked to gut disorders such as IBD (1).

2. Gut disorders

Several studies have shown that gut dysbiosis – including a less diverse gut microbiota and lower numbers of short-chain fatty acid-producing bacteria – is associated with intestinal diseases such as irritable bowel syndrome (IBS), Crohn’s disease, and inflammatory bowel disease (IBD) (1, 2, 3).

Bacteria in the gut produce gas as a by-product, which can cause bloating, cramping, and intestinal discomfort in the host. With chronic gut disorders such as IBS, these symptoms are exacerbated, possibly due to overpopulation of certain bacteria species in the gut, and underpopulation of others, such as short-chain fatty acid-producing bacteria.

Additionally, the chronic gut inflammation associated with IBD is thought to be linked to the disrupted immune regulation that comes with gut dysbiosis.

3. Immune system

The gut microbiome interacts closely with the immune system. Imbalances in the gut microbiome can bring on unwarranted immune signalling and inflammation.

In particular, the short-chain fatty acids produced by gut bacteria are extremely important for communicating with the immune system and regulating the immune response (4).

Research has shown that certain gut bacteria (species of Clostridia) can promote the production of anti-inflammatory T regulatory immune cells (5). The generation of these cells is facilitated by a short-chain fatty acid called butyrate.

4. Autoimmune diseases

Autoimmune diseases are diseases where the immune system mistakenly attacks your own body.

Given the role that gut bacteria have in immune regulation, it makes sense that those with autoimmune conditions tend to have disrupted gut microbiomes.

Studies show that gut dysbiosis (less diverse microbiome) is associated with autoimmune diseases such as type 1 diabetes, multiple sclerosis, and rheumatoid arthritis (6, 7, 8).

5. Nervous system

Research has also discovered that the gut microbiome actually interacts with the brain and nervous system.

The gut and the brain are in constant communication with each other, and can influence each other’s behaviour.

Animal studies suggest that the gut microbiome plays a role in things like mood regulation, anxiety, and cognition.

Additionally, some animal studies suggest that a disturbed gut microbiota is linked to neurological disorders such as Alzheimer’s and Parkinson’s disease. Human studies are currently lacking, but researchers are looking into the potential gut microbiome-based therapies for neurodegenerative disorders (9, 10).

6. Weight

Gut bacteria also influence the body’s ability to extract and store calories, and thus may play a role in weight gain, obesity, and associated conditions.

A less diverse gut microbiome is associated with long-term weight gain in humans (11). This study found that high microbiome diversity and high fibre intake are associated with lower long-term weight gain.

Additionally, several studies have shown the association between lower gut diversity and obesity, weight gain, insulin resistance, prediabetes, and type 2 diabetes (12, 13).

7. Leaky gut

A common term being thrown around with regards to gut health these days, is leaky gut.

Leaky gut syndrome refers to a condition where the permeability of the intestine wall is increased. Bacteria and bacterial toxins called endotoxins are able to leak through the intestinal barrier and migrate from your gut to your bloodstream.

Once in the bloodstream, these out-of-place molecules are thought to then activate the immune system, consequently leading to chronic inflammation.

Leaky gut and the resulting chronic inflammation, are often thought to be the underlying cause of many chronic conditions.

However, more supporting evidence is still needed, and medical professionals are not always in agreement as to whether leaky gut is a legitimate diagnosable condition.

How to Maintain a Healthy Gut Microbiome

A healthy gut starts with the food you put into your gut.

You want to make sure you are eating a good balance of food to maintain a high diversity of bacteria species and high numbers of healthy bacteria.

The standard Western diet tends to contain excessive amounts of sugar and fat, which can harm the microbiome by breeding the bacteria that feed off sugar and fat.

One study compared the effects on the gut microbiome of a “healthy diet” consisting of high consumption of fruits, yogurt, and soups, and low consumption of sugary drinks, vs. an “unhealthy diet” consisting of high consumption of sugary drinks and low consumption of fruits, yogurt, and water (14). Not surprisingly, the healthy diet resulted in greater gut microbiome diversity (and the added bonuses of lower inflammation and LDL cholesterol).

In short, ditch highly sugary and processed foods, and replace them with whole foods.

Maintain healthy populations of gut bacteria by including plenty of fibre-rich foods in your diet (15). Dietary fibre consumption will help breed those good bacteria that can digest it into those short-chain fatty acids that you want. Fibre-rich foods include fruits, vegetables, legumes, whole grains, nuts, and seeds.

Eating fermented foods such as kefir and sauerkraut are also great for helping maintain healthy bacteria species in your gut.

Other tips:

  • Probiotic and prebiotic supplements can help restore healthy, live bacteria (probiotics) to your gut, and provide food (prebiotics) for the bacteria in your gut. However, note that taking a supplement is no comparison to consuming the natural probiotics in fermented foods, or the natural prebiotic that is fibre.
  • Aspartame and some other artificial sweeteners have been shown to disrupt the gut microbiome.
  • Antibiotics can really mess up the gut microbiota, as they kill both good and bad bacteria. Of course, take antibiotics if you need them, but make an effort to help restore a healthy microbiome after.
  • In more extreme cases of gut dysbiosis, faecal transplants are used to help restore the gut microbiome.
  • Lastly, play in the dirt! This is more applicable for babies and young children, but it is so important for kids to be exposed to all the microbes that are out there in the dirt. Playing in the dirt (and occasionally eating dirt) is crucial for the early development of a healthy, diverse microbiome.


The gut microbiome is the collection of all the microorganisms living in the gut. These microorganisms play important, beneficial roles in human digestion, immune responses, and more. Disruption of the gut microbiome is associated with chronic health conditions such as gut disorders, autoimmune diseases, diabetes, obesity, and more. Maintain a healthy gut by eating a balanced, whole-food diet high in fibre and fermented foods.

That’s it for this article on the gut microbiome! If you enjoyed this article or have any questions, drop a comment down below!

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